. 2011 Jul;77(13):4626–4633. doi: 10.1128/AEM.02232-10

Table 3.

nodD primers for specific amplification of Rhizobium leguminosarum bv. trifolii and bv. viciae and number of BLAST hits scoring 100% identity and percent identity with top nontarget hit

Primer name	Target	Primer sequence(s)^a	Length (bp)	T_m (°C)	% GC	No. of 100% BLAST hits		Top nontarget hit, % identity
Primer name	Target	Primer sequence(s)^a	Length (bp)	T_m (°C)	% GC	Target	Clones or R. leguminosarum. sp.	Top nontarget hit, % identity
nodD trifolii F235	R. leguminosarum bv. trifolii	CSGATTTCATGACGCTBGTATTC	22	59	43	9 (total)	10
		CcGATTTCATGACGCTcGTATTC				3	4	91
	Degeneracies for nodD trifolii	CgGATTTCATGACGCTcGTATTC				1		78
	F235 primer	CgGATTTCATGACGCTtGTATTC				1	1	73
		CcGATTTCATGACGCTgGTATTC				2	5	78
		CgGATTTCATGACGCTgGTATTC				2		82
nodD trifolii R566	R. leguminosarum bv. trifolii	GCCGCTTAAAACCGTGCTC	18	59	58	9	11	89
nodD viciae F88	R. leguminosarum bv. viciae	TGCAGAGACGGGAGCTARTTC	21	58	52	85	55	81
nodD viciae R328	R. leguminosarum bv. viciae	TCGTCAAGTGGCAGCAACTC	20	59	55	84	62	80
nodD viciae F443	R. leguminosarum bv. viciae	GACGCACACCAGTCTCTCTTCG	22	61	59	80	60	77
nodD viciae R662	R. leguminosarum bv. viciae	GGGGATGGTTGCTATTCGAT	20	57	60	79	46	90

Lowercase letters indicate site of degeneracy.